Jak 2 did it for me.Last boss for me consisted of JUMP SPINKICK SHOOT JUMP SPINKICK SHOOT JUMP SPINKICK SHOOT JUMP SPINKICK SHOOT JUMP SPINKICK SHOOT JUMP SPINKICK SHOOT.X and square button never worked the same way after that

Super Mario 64. In the last battle with Bowser, you pick him up by the tail and twirl him around in circles, throwing him onto some bombs around the arena. To spin him around you...spin around the analog stick. Aggressively. It's mid combat! I lost a few controllers to that.

shadow the hedgehog had some of the WORST camera angles and controls i have ever seen.
mario party 1 destroyed my controller and gave me blisters. (had to get a new one. gg nintendo)
can't think of any others offhand.